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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggcaactgtcacaaattgcctgatatttatgctcatttttcctcctaatttttccaattttgcagGCTGCAAAGCCTGATGAGCCAAGTTGGGACAGCCCATGGGGTCCTGGAAGACCGGGATGGCACATAGAGTGCAGTGCAATGAGTGCACATTATTTGACCT

Basic information

species Vitis vinifera
transcript Vv03s0017g01640.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0017g01640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g04960.4 (Oryza sativa), 3'ss of exon 3
---------gtgg-gcaactgtcacaaattgcctg-atatttatgctcatttttcctcctaatttttccaat-tttgcagGCTGCAAAGCCTGATGAGCCAAGTTGGGACAGCCCATGGGGTCCTGGAAGACCGGGATGGCACATAGAGTGCAGTGCAATGAGTGCACATTATTTGACCT
          ||     |   ||| | ||  | || | |||  | ||   |  |  || |   | |   | | | | |||||||| |||   |  || ||    ||||| ||||||||||| | ||| ||||| |||||||| || || ||||||||||||||||| ||||||||     
gtaattttgatgttatgatattcatagatctcttgcacattgttactttctgcttatcttttctgtattattgtattcagGCTGCTAAGGAAGGCGAACCTTTCTGGGATAGCCCATGGGGCCGTGGTAGACCAGGATGGCATATTGAATGCAGTGCAATGAGTGCTCATTATTTAGGAC

upper sequence: Vv03s0017g01640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os10g32570.1 (Oryza sativa), 3'ss of exon 4
----------gtgggcaactgtcacaaattgcctgatat----ttatgctcatttttcctcctaa--tttttccaattttgcagGCTGCAAAGCCTGATGAGCCAAGTTGGGACAGCCCATGGGGTCCTGGAAGACCGGGATGGCACATAGAGTGCAGTGCAATGAGTGCACATTATTTGACCT
          |    ||  |    |||| |  |  || |     | | |||  | ||| |  ||   || |      | ||||| |||| |||   | |||||||  |||||| ||||| ||||||| |||||| || |||||||| || ||||||||||| ||||| || |||||||||    
gtgacatactgctttcactttaaccaaacttacccatttgagcctcttctctgtattcttgatagacttgtattgtctgtgcagTCTGCTAAGGAGGGTGAGCCATCTTGGGAGAGCCCTTGGGGTCGTGGAAGGCCAGGATGGCATATTGAGTGCAGTGCGATGAGCGCTCATTATTTGGGTA

upper sequence: Vv03s0017g01640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G071924_T01 (Zea mays), 3'ss of exon 1
---------------------gtgg--gcaactgtcacaaattgcctgatattta------tgctca-tttttcctcctaatttttc--caattttgcagGCTGCAAAGCCTGATGAGCCAAGTTGGGACAGCCCATGGGGTCCTGGAAGACCGGGATGGCACATAGAGTGCAGTGCAATGAGTGCACATTATTTGACCT
                      | |  | |  | |   ||||   || |||| ||      || ||| ||||| ||  || ||  |   | || || ||||||||||||   |  || ||   |||||| ||||| ||||| | |||||||||||||||||| || || ||||| ||||||||||| || |||||     
tttgtgaaactttaggcaaaaatagctgtagttttgtgaaataaactcatatctagcagtgtggtcacttttttcttatacttcattaaccatgtttcagGCTGCAAAGGAGGGCGAACCTTTTTGGGATAGCCCTTGGGGCCGTGGAAGACCGGGATGGCATATTGAATGCAGCGCAATGAGTGCTCACTATTTAGGAC

upper sequence: Vv03s0017g01640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G41880.2 (Glycine max), 3'ss of exon 2
----------------gtgggcaactgtcacaaattgcc-tgatatttatgctcatttttcctcctaatttttccaattttgcagGCTGCAAAGCCTGATGAGCCAAGTTGGGACAGCCCATGGGGTCCTGGAAGACCGGGATGGCACATAGAGTGCAGTGCAATGAGTGCACATTATTTGACCT
                    |  | | | ||| |||    | | ||||  | ||  |  |  | || | |  |  |   ||||||||||| || || | |||||| || ||||||||||| ||||||||||||||||| || |||||||| ||||||||||||||||||||   |||||| ||  
gtgtgagagaacctttaccagttattttaacatattttagtaacatttgagatctctcatatttctcaataataaataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGACCTGGGTGGCACATTGAGTGCAGTGCAATGAGTGCTTGTTATTTAACTC

upper sequence: Vv03s0017g01640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G25160.1 (Glycine max), 3'ss of exon 4
--------------gtgggcaactgtcacaaattgcc-tgatatttatgctcattt---ttcctcctaatttttccaat----tttgcagGCTGCAAAGCCTGATGAGCCAAGTTGGGACAGCCCATGGGGTCCTGGAAGACCGGGATGGCACATAGAGTGCAGTGCAATGAGTGCACATTATTTGACCT
                  |  | | | ||| |||    | | ||||    ||  |    || ||  |||| ||   |||     ||||||||||| || || | |||||| || ||||||||||| ||||||||||||||||| || |||||||| || |||||||||||||||||   |||||| ||  
gtgcgagaacctttaccagttattttaacatattttagtaacatttgaaatctctgacatttcttataatattaataatgataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGACCTGGGTGGCACATTGAATGCAGTGCAATGAGTGCTTGTTATTTAACTC

upper sequence: Vv03s0017g01640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G32200.1 (Glycine max), 3'ss of exon 2
gtgggcaactgtcacaaattgcctgatatttatgctcatttttcctcctaatttttccaattttgcagGCTGCAAAGCCTGATGAGCCAAGTTGGGACAGCCCATGGGGTCCTGGAAGACCGGGATGGCACATAGAGTGCAGTGCAATGAGTGCACATTATTTGACCT-------------
                                       |   ||  |||||||| |  ||| || |  ||   || || |  ||||| |||||||||| ||| |||| ||||||||| || || |||||||| || |||||||||||||||||   |||||| ||               
--------------------------------------gtaacccaactaattttgc--attgtggaatct---aaaccagGCGAGCCTAGTTGGGACAACCCTTGGGATCCTGGAAGTCCTGGGTGGCACATTGAATGCAGTGCAATGAGTGCTTGTTATTTAACTCATAAATTTGATAT

upper sequence: Vv03s0017g01640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G38830.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------gtgggcaactgtcacaaattgcctgatatttatgct-catttttcctcctaatttttc----caatttt--gcagGCTGCAAAGCCTGATGAGCCAAGTTGGGACAGCCCATGGGGTCCTGGAAGACCGGGATGGCACATAGAGTGCAGTGCAATGAGTGCACATTATTTGACCT
              |       | | | |       |||   ||   |   || |       | |  |||      |||| |  |||||| |||||||||||||||||||||||||| ||||| |||||||| |||||||| ||||||||||| |||||||||||||||||||  |||||| || |  
gtttgaatatcttttttctttttattatattcaatttgaggcttgcacagtatatgatgaagtgaagtttgaacataattctatgcagGCGGCAAAGCCTGATGAGCCAAGTTGGGAGAGCCCTTGGGGTCCAGGAAGACCAGGATGGCACATCGAGTGCAGTGCAATGAGTGTTCATTATCTGTCTC

upper sequence: Vv03s0017g01640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G56300.1 (Arabidopsis thaliana), 3'ss of exon 4
-gtgggcaactgtca-caaattgcctgatatttatgctcattttt---------cctcctaatttt----tccaattt---tgcagGCTGCAAAGCCTGATGAGCCAAGTTGGGACAGCCCATGGGGTCCTGGAAGACCGGGATGGCACATAGAGTGCAGTGCAATGAGTGCACATTATTTGACCT
  | | ||| | | | |   |||    ||  ||||     || ||         |  |   | |||    |  |||||   |||||||||||||  ||| ||| ||||||||||| ||||| ||||||| ||||||||| ||||||||||| ||                                
gtttgacaagtttaatctttttgttcaattcttatttcagttattaaactagagcagctggagtttatgctgaaatttttatgcagGCTGCAAAATCTGGTGAACCAAGTTGGGAGAGCCCTTGGGGTCATGGAAGACCAGGATGGCACATCGA--------------------------------

upper sequence: Vv03s0017g01640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S504_12V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------gtgggcaa----ctgtcacaaattgcctgatatttatgctca----tttttcctcctaatttttccaat--------tttgcagGCTGCAAAGCCTGATGAGCCAAGTTGGGACAGCCCATGGGGTCCTGGAAGACCGGGATGGCACATAGAGTGCAGTGCAATGAGTGCACATTATTTGACCT
                                                               | | | |     ||||  |        | | ||  | ||||    || |  |||  ||  |  |   |         | ||||  ||| || || |  |||||   ||||||||| || |||||||||||  | ||||| |||||||| || |||||||| ||||||||  |  ||||     
gtcagcgcccttgaaaatggtgagagaaaactcttctgtctgctgagttaggtcctagggaattagactaaatcttgtcctactaaagtgggtgttggttctcaaattttctctctctgaaggtcgctggtatcattttctcgcagAGTGCGAAACCCGGAGAGCCTGCTTGGGACAGTCCTTGGGGTCCTGGGCGCCCGGGCTGGCACATTGAATGCAGTGCTATGAGTGCGGAGCATTTAGGTC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|161718417|gb|FC067293.1|FC067293
EST:     TTGCTGTTGATTCAAGAAAGCGAAATCCAGCTGACTTCGCATTGTGGAAG                         GCTGCAAAGCCTGATGAGCCAAGTTGGGACAGCCCATGGGGTCCTGGAAGA
genomic: TTGCTGTTGATTCAAGAAAGCGAAATCCAGCTGACTTCGCATTGTGGAAGgtgggcaact ... aattttgcagGCTGCAAAGCCTGATGAGCCAAGTTGGGACAGCCCATGGGGTCCTGGAAGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaattgcctgatatttatgctcatttttcctcctaatttttccaattttgcagGCTGCAAAGCCTGATGAGCCAAGTTGGGACAGCCCATGGGGTCCTGGAAGACCGGGATGGCACATAGAGTGCAGTGCAATGAGTGCACATTATTTGACCT
                                tcctaat  putative branch site (score: 2)
                         tttttcctcctaattt  CT-rich tract
                                   taatttttccaatttt  TA-rich tract